She closed her set at Marlins Park by dedicating a performance of "Halo" to the rapper, who was in the audience.
"I want to dedicate this song to my beautiful husband," she said. "Boo boo, I love you so much."
The couple has been the subject of infidelity rumors thanks to the singer's new album, "Lemonade."
Earlier in the night, Bey sang the "Lemonade" track that spurred much speculation about the state of her marriage, "Sorry" -- which includes the now-famous lyric, "He better call Becky with the good hair."
"Prince, thank you for your beautiful music," she said. "God, thank you for speaking through a beautiful artist that inspired all of us."
At one point, "Purple Rain" was played during a costume change break, with a screen on stage displaying the color purple.
The Formation World Tour continues Friday in Tampa.